Merge pull request #5 from shervinea/syntax-cleanup

Readability and syntax cleanup
shervinea · Sep 7, 2021 · fcf6aab · fcf6aab
2 parents bec8ca3 + cd06ad1
commit fcf6aab
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diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,19 @@
+# Mac.
 **/.DS_Store
+
+# Notebooks.
 **/.ipynb_checkpoints
+
+# PDB caching.
+*.pdb
+
+# Code execution.
 **/__pycache__
 **/.pyc
+.idea/**
+
+# Package.
 *.egg-info
+
+# Virtual environment.
+venv/**
diff --git a/datasets/charge.csv b/datasets/charge.csv
diff --git a/datasets/download_pdb.txt b/datasets/download_pdb.txt
diff --git a/datasets/hydropathy.csv b/datasets/hydropathy.csv
diff --git a/datasets/isoelectric.csv b/datasets/isoelectric.csv
diff --git a/datasets/make_files/charge.py b/datasets/make_files/charge.py
diff --git a/datasets/make_files/download_pdb.py b/datasets/make_files/download_pdb.py
@@ -1,24 +1,19 @@
-'Converts list of PDB enzymes in a text file'
+"""Converts list of PDB enzymes in a text file."""
 
 # Authors: Afshine Amidi <[email protected]>
 #          Shervine Amidi <[email protected]>
 
 # MIT License
 
-import pandas as pa
-import csv
-from enzynet.tools import read_dict
+import pandas as pd
 
 
-# Read csv files
-df = pa.read_csv('../dataset_all.csv', header=None)
+def create_download_file() -> None:
+    """Creates the RCSB download file containing all relevant PDB IDs."""
+    df = pd.read_csv('../dataset_all.csv', header=None)
+    with open('../download_pdb.txt', 'w') as file:
+        file.write(", ".join(df[0].tolist()))
 
-# Only keep PDB IDs
-df = df[0]+', '
-df = df.tolist()
 
-# Save to text file with one PDB ID per line
-file = open('../download_pdb.txt','w')
-for i in range(len(df)):
-    file.write(df[i])
-file.close()
+if __name__ == "__main__":
+    create_download_file()